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Zinc in PDB 4hx3: Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin

Enzymatic activity of Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin

All present enzymatic activity of Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin:
3.4.24.77;

Protein crystallography data

The structure of Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin, PDB code: 4hx3 was solved by S.Trillo-Muyo, S.Martinez-Rodriguez, J.L.Arolas, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.49 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.540, 121.810, 130.670, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 24.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin (pdb code 4hx3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin, PDB code: 4hx3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4hx3

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Zinc binding site 1 out of 6 in the Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:32.9
occ:1.00
 OD1 A:ASP93 1.9 32.9 1.0
NE2 A:HIS87 2.1 35.4 1.0
NE2 A:HIS83 2.1 33.3 1.0
O A:HOH323 2.2 28.7 1.0
CG A:ASP93 2.8 34.2 1.0
CE1 A:HIS87 3.0 35.2 1.0
CD2 A:HIS83 3.0 33.7 1.0
OD2 A:ASP93 3.1 44.9 1.0
CE1 A:HIS83 3.1 33.5 1.0
CD2 A:HIS87 3.2 35.9 1.0
OE2 A:GLU84 3.8 44.1 1.0
O B:ALA32 3.9 39.9 1.0
O B:HOH206 4.0 33.5 1.0
OE1 A:GLU84 4.1 43.4 1.0
ND1 A:HIS87 4.1 36.3 1.0
CG A:HIS83 4.2 33.3 1.0
CB A:ASP93 4.2 32.9 1.0
ND1 A:HIS83 4.2 34.7 1.0
CG A:HIS87 4.2 34.2 1.0
CD A:GLU84 4.3 46.1 1.0
NE2 B:HIS3 4.6 49.0 1.0
C B:ALA32 4.7 38.0 1.0
OH A:TYR95 4.8 35.5 1.0
CE1 B:HIS3 4.8 48.1 1.0
CA B:TYR33 4.8 31.4 1.0
CE A:MET103 4.8 29.7 1.0
CA A:ASP93 4.9 31.3 1.0

Zinc binding site 2 out of 6 in 4hx3

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Zinc binding site 2 out of 6 in the Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:43.8
occ:1.00
 OD1 C:ASP93 1.9 50.0 1.0
O C:HOH302 1.9 38.8 1.0
NE2 C:HIS83 2.1 35.9 1.0
NE2 C:HIS87 2.1 39.0 1.0
CG C:ASP93 2.8 48.7 1.0
CE1 C:HIS87 3.0 39.8 1.0
CD2 C:HIS83 3.0 35.8 1.0
OD2 C:ASP93 3.0 50.7 1.0
CE1 C:HIS83 3.1 36.7 1.0
CD2 C:HIS87 3.2 40.1 1.0
OE2 C:GLU84 3.7 53.3 1.0
O D:ALA32 3.8 48.1 1.0
OE1 C:GLU84 4.2 52.3 1.0
ND1 C:HIS87 4.2 42.1 1.0
CG C:HIS83 4.2 35.1 1.0
CB C:ASP93 4.2 41.4 1.0
ND1 C:HIS83 4.2 37.3 1.0
CD C:GLU84 4.2 53.6 1.0
CG C:HIS87 4.2 40.7 1.0
C D:ALA32 4.6 44.3 1.0
CA D:TYR33 4.6 36.4 1.0
OH C:TYR95 4.7 42.4 1.0
CE1 D:HIS3 4.7 71.9 1.0
NE2 D:HIS3 4.8 70.5 1.0
CE C:MET103 4.8 41.1 1.0
CA C:ASP93 4.9 42.1 1.0

Zinc binding site 3 out of 6 in 4hx3

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Zinc binding site 3 out of 6 in the Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:50.7
occ:1.00
 OD1 E:ASP93 1.9 54.1 1.0
NE2 E:HIS87 2.0 50.3 1.0
NE2 E:HIS83 2.1 49.8 1.0
O E:HOH309 2.1 28.1 1.0
CG E:ASP93 2.8 54.5 1.0
CE1 E:HIS87 2.9 50.8 1.0
CD2 E:HIS83 3.0 50.4 1.0
OD2 E:ASP93 3.1 59.1 1.0
CE1 E:HIS83 3.1 50.0 1.0
CD2 E:HIS87 3.1 51.6 1.0
OE2 E:GLU84 3.8 64.8 1.0
O F:ALA32 3.9 46.9 1.0
O F:HOH204 4.1 37.1 1.0
ND1 E:HIS87 4.1 53.0 1.0
CG E:HIS83 4.2 49.5 1.0
CB E:ASP93 4.2 46.8 1.0
CG E:HIS87 4.2 51.4 1.0
OE1 E:GLU84 4.2 63.0 1.0
ND1 E:HIS83 4.2 51.4 1.0
CD E:GLU84 4.3 72.5 1.0
C F:ALA32 4.7 45.8 1.0
CA F:TYR33 4.7 40.6 1.0
OH E:TYR95 4.8 38.1 1.0
CE E:MET103 4.8 48.4 1.0
NE2 F:HIS3 4.8 85.1 1.0
CA E:ASP93 4.8 46.9 1.0
CE1 F:HIS3 5.0 83.7 1.0

Zinc binding site 4 out of 6 in 4hx3

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Zinc binding site 4 out of 6 in the Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn201

b:41.6
occ:1.00
 OD1 G:ASP93 1.9 38.6 1.0
NE2 G:HIS83 2.0 34.1 1.0
NE2 G:HIS87 2.0 31.7 1.0
O G:HOH311 2.2 25.1 1.0
CG G:ASP93 2.8 43.5 1.0
CE1 G:HIS87 2.9 31.7 1.0
CD2 G:HIS83 3.0 34.8 1.0
CE1 G:HIS83 3.1 34.9 1.0
OD2 G:ASP93 3.1 52.1 1.0
CD2 G:HIS87 3.1 32.4 1.0
O H:ALA32 3.8 38.3 1.0
OE2 G:GLU84 3.8 42.8 1.0
O H:HOH204 4.0 44.7 1.0
CG G:HIS83 4.1 34.7 1.0
ND1 G:HIS87 4.1 32.8 1.0
CB G:ASP93 4.2 41.5 1.0
ND1 G:HIS83 4.2 36.5 1.0
OE1 G:GLU84 4.2 55.8 1.0
CG G:HIS87 4.2 31.6 1.0
CD G:GLU84 4.3 46.3 1.0
C H:ALA32 4.6 36.5 1.0
CA H:TYR33 4.7 33.5 1.0
NE2 H:HIS3 4.7 51.9 1.0
CE G:MET103 4.7 30.7 1.0
OH G:TYR95 4.8 32.0 1.0
CA G:ASP93 4.8 40.1 1.0
CE1 H:HIS3 4.9 51.6 1.0

Zinc binding site 5 out of 6 in 4hx3

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Zinc binding site 5 out of 6 in the Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:36.6
occ:1.00
 OD1 I:ASP93 2.0 37.5 1.0
NE2 I:HIS87 2.1 33.9 1.0
NE2 I:HIS83 2.1 37.3 1.0
O I:HOH312 2.4 36.9 1.0
CG I:ASP93 2.9 37.6 1.0
CD2 I:HIS83 3.0 37.3 1.0
CE1 I:HIS87 3.0 34.2 1.0
OD2 I:ASP93 3.1 42.7 1.0
CD2 I:HIS87 3.2 34.8 1.0
CE1 I:HIS83 3.2 37.2 1.0
OE1 I:GLU84 3.8 50.1 1.0
O J:ALA32 3.9 42.6 1.0
O J:HOH602 3.9 35.1 1.0
OE2 I:GLU84 4.2 58.1 1.0
CG I:HIS83 4.2 35.9 1.0
CD I:GLU84 4.2 51.5 1.0
ND1 I:HIS87 4.2 36.0 1.0
CG I:HIS87 4.3 34.8 1.0
CB I:ASP93 4.3 33.5 1.0
ND1 I:HIS83 4.3 37.8 1.0
NE2 J:HIS3 4.5 51.9 1.0
C J:ALA32 4.7 41.6 1.0
CA J:TYR33 4.8 36.8 1.0
CE1 J:HIS3 4.8 50.8 1.0
OH I:TYR95 4.8 34.5 1.0
CE I:MET103 4.9 32.3 1.0

Zinc binding site 6 out of 6 in 4hx3

Go back to Zinc Binding Sites List in 4hx3
Zinc binding site 6 out of 6 in the Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Streptomyces Caespitosus Sermetstatin in Complex with S. Caespitosus Snapalysin within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn201

b:58.6
occ:1.00
 OD1 K:ASP93 1.9 59.1 1.0
O K:HOH301 1.9 36.7 1.0
NE2 K:HIS87 1.9 56.6 1.0
NE2 K:HIS83 2.0 62.9 1.0
CG K:ASP93 2.8 59.6 1.0
CE1 K:HIS87 2.8 57.9 1.0
CD2 K:HIS83 3.0 63.6 1.0
CD2 K:HIS87 3.0 58.4 1.0
OD2 K:ASP93 3.1 65.3 1.0
CE1 K:HIS83 3.1 64.0 1.0
OE1 K:GLU84 3.9 58.7 1.0
O L:ALA32 3.9 51.7 1.0
ND1 K:HIS87 4.0 61.5 1.0
CG K:HIS87 4.1 60.1 1.0
CG K:HIS83 4.1 63.0 1.0
CB K:ASP93 4.2 56.8 1.0
OE2 K:GLU84 4.2 72.6 1.0
ND1 K:HIS83 4.2 65.3 1.0
CD K:GLU84 4.3 75.5 1.0
CE1 L:HIS3 4.7 59.3 1.0
CE K:MET103 4.7 69.0 1.0
C L:ALA32 4.7 50.5 1.0
NE2 L:HIS3 4.7 57.6 1.0
CA L:TYR33 4.8 47.6 1.0
OH K:TYR95 4.8 51.2 1.0
CA K:ASP93 4.8 58.0 1.0

Reference:

S.Trillo-Muyo, S.Martinez-Rodriguez, J.L.Arolas, F.X.Gomis-Ruth. Mechanism of Action of A Janus-Faced Single-Domain Protein Inhibitor Simultaneously Targeting Two Peptidase Classes Chem Sci V. 4 791 2013.
ISSN: ISSN 2041-6520
DOI: 10.1039/C2SC21712K
Page generated: Wed Dec 16 05:22:59 2020

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